The historical situation isn't modelled whatsoever in CK II, which is why the East African states are effectively unplayable, especially when you take into account just how absurdly/ahistorically overpowered and expansionist the Fatimids are. The Fatimids were a Shi'a dynasty ruling over a predominantly Christian and Sunni populace and surrounded by Sunni states. Pretty much everyone around them hated them -- with the notable exception of the Nubians, who traded gold and slaves (making up a sizeable chunk of the Fatimid army) in exchange for a sort of mutual defensive alliance (the
Baqt). In some gameplay elements it can be ignored (for example, it wasn't an offensive alliance and therefore you shouldn't be able to play as Nubia and drag the Fatimids into any wars you start)
but it was crucial in the sense that the Fatimids had friendly relations with the rulers of Nubia and swore to protect them from external threats.
So yeah, the Fatimids should not be declaring any sort of wars against the Nubians on the basis that they had a formal alliance and were one another's
only friends.
Combine that with the current AI trend of spamming
offensive, expansionist Jihads and you basically have an absurd, broken Middle East setup/mentality.